The Essential Guide to Women’s Gut Health

From a Naturopathic Doctor’s Perspective

As a naturopathic doctor specializing in women’s health and hormones, one of the most impactful—yet often overlooked—areas I focus on with my patients is the gut. We often think of gut health in terms of digestion alone: bloating, gas, constipation, and food sensitivities. But the truth is, your gut is at the center of your overall well-being, playing a profound role in hormone balance, mood, energy, immunity, skin health, and even fertility.

Gut health is especially important for women. Between fluctuating hormones, stress, dietary pressures, birth control use, pregnancy, and autoimmune conditions (which disproportionately affect women), we are uniquely vulnerable to imbalances in the gut microbiome and gut lining integrity. In this guide, I’ll walk you through why gut health matters for women at every stage of life, how to recognize when something is off, and what steps you can take to support vibrant gut and whole-body wellness.

Why the Gut is the Foundation of Women's Health

At first glance, your gut seems simple: it's where food gets digested and absorbed. But dig a little deeper, and you'll see it’s so much more than that. The gut is:

• The home of 70% of your immune system

• Where most of your neurotransmitters (like serotonin) are made

• The primary site for hormone metabolism and detoxification

• A key regulator of inflammation throughout the body

In other words, when your gut is in balance, your immune system, mood, hormones, and skin thrive. When it’s out of balance, symptoms can manifest in nearly every body system—and often, they don’t seem like they’d be connected to digestion at all.

How Female Hormones Are Affected by the Gut

There is a bidirectional relationship between your gut and your hormones. Estrogen, progesterone, and even testosterone influence the gut microbiome, motility, and inflammation—and vice versa.

The Estrobolome Connection

One of the most important links is through the estrobolome—a subset of gut bacteria responsible for metabolizing and recycling estrogen. When the estrobolome is healthy, it helps ensure your body maintains appropriate estrogen levels by detoxifying and eliminating excess hormones.

However, if your gut microbiome is imbalanced (due to dysbiosis, antibiotics, chronic stress, or a low-fiber diet), estrogen metabolism can become sluggish. The result? Estrogen gets reabsorbed into circulation, contributing to estrogen dominance—a root cause of symptoms like:

• PMS

• Heavy or painful periods

• Fibroids or endometriosis

• Breast tenderness

• Weight gain around hips and thighs

This is why I always look to the gut when addressing hormonal imbalances in women. You can’t balance hormones without also addressing how they are processed and excreted through the digestive system.

The Impact of Stress and the Gut-Brain Axis

Many women I see in practice are juggling careers, families, relationships, and expectations—often leaving little room for rest and nourishment. Chronic stress has a major impact on gut health via the gut-brain axis.

When you’re in fight-or-flight mode, your body diverts energy away from digestion. This leads to:

• Decreased stomach acid production

• Slower motility

• Impaired absorption of nutrients

• Suppression of healthy gut bacteria

On top of that, stress disrupts your gut lining and contributes to intestinal permeability (leaky gut), which increases inflammation and food sensitivities. Over time, this can impact not just digestion, but mood (anxiety, depression, brain fog), immunity, and even thyroid function.

Nurturing your gut means supporting your nervous system as well. Practices like mindful eating, breathwork, yoga, and restorative sleep can dramatically improve gut function and overall wellness.

The Gut-Skin-Hormone Triangle

If you’re struggling with acne, eczema, rosacea, or even psoriasis, the solution may not be more skincare—it may be gut care.

Your skin, like your hormones, is intricately connected to what’s happening in your gut. Dysbiosis and leaky gut can drive systemic inflammation that shows up as skin breakouts, rashes, or sensitivity. On top of that, gut issues can worsen hormonal imbalances, contributing to hormonal acne and cyclical flares.

In clinical practice, I often see that when we work on balancing the microbiome, improving nutrient absorption, and supporting detox pathways, chronic skin issues clear up beautifully.

Key Signs Your Gut May Be Out of Balance

Even if you’re not experiencing traditional digestive symptoms, your gut may still need support. Some common signs of gut dysfunction include:

• Bloating or gas, especially after meals

• Constipation or loose stools

• Fatigue or low energy

• Brain fog or anxiety

• Irregular or painful periods

• Acne, rashes, or skin sensitivity

• Joint pain or autoimmune symptoms

• Food sensitivities or unexplained weight changes

If you’re experiencing a combination of these symptoms, it’s time to take a deeper look at your gut.

Essential Steps to Support Women's Gut Health

The good news? The gut is incredibly responsive to lifestyle, dietary, and therapeutic support. Here’s where I recommend women begin:

1. Prioritize a Gut-Friendly Diet

Food is the foundation. A gut-healing diet emphasizes:

• Colorful vegetables and fruits (rich in antioxidants and polyphenols)

• Fermented foods like sauerkraut, kimchi, and kefir (for healthy bacteria)

• Fiber-rich foods (like flaxseed, chia, oats, and leafy greens) to feed good gut flora

• Anti-inflammatory fats like olive oil, avocado, nuts, and wild salmon

• Bone broth and collagen to support gut lining integrity

Avoid processed foods, refined sugars, alcohol, and artificial additives, which disrupt gut flora and promote inflammation.

2. Balance Your Microbiome

You can nourish your microbiome through both prebiotics (fiber that feeds good bacteria) and probiotics (beneficial bacteria themselves). While food is ideal, some women benefit from probiotic supplementation—especially after antibiotics or if they’re experiencing chronic symptoms.

Fiber is an important part of our diet that nourishes our good bacteria and ensures a healthy microbiome. I recommend my patients get around 50 grams of fiber/day. 

But probiotics are not a one-size-fits-all all. Some patients will feel worse with probiotics. In my practice. Additionally, some probiotic strains can increase histamine levels, and trigger folks who are sensitive to it. And I am seeing more and more patients with histamine intolerance. For these reasons, I rely heavily on functional GI testing to guide my approach to each patient's individual needs when it comes to supporting their microbiome. 

3. Support Digestion

Low stomach acid and enzyme production are common in stressed or depleted women. You can support digestion with:

• Bitter herbs before meals

• Apple cider vinegar or lemon water

• Digestive enzymes, especially when eating heavier meals

• Mindful eating (sit down, chew thoroughly, avoid multitasking)

  
  

4. Heal the Gut Lining

To restore gut integrity and reduce inflammation, I often use:

• L-glutamine

• Zinc carnosine

• Marshmallow root or deglycyrrhizinated licorice (DGL)

• Omega-3 fatty acids

• Vitamin A and D (for mucosal immune function)

These nutrients work synergistically to calm inflammation, tighten the gut barrier, and reduce sensitivity to foods and stressors.

5. Reduce Stress and Restore the Nervous System

This is essential. Chronic stress impairs digestion, suppresses immunity, and wrecks hormone balance. To support gut and hormonal healing, you need to regulate your nervous system.

Make space for:

• Restorative movement like walking or yoga

• Meditation, breathwork, or journaling

• Social connection and time in nature

• Adequate sleep (7–9 hours per night)

• Healthy boundaries with your time and energy

  
  

6. Give your gut a rest

A network of nerves innervates our gut called the migrating motor complex, which is responsible for helping our intestines move regularly so that they can efficiently eliminate and maintain a healthy balance of the microbiome. The migrating motor complex works between meals and at night while we are fasting. That means our gut needs a break from taking in food to do its best work. To learn more, check out my blog post that talks all about this system and how to support it! 

When to Seek Deeper Support

If you've tried the basics and still struggle with gut symptoms, it's worth digging deeper. In my practice, I use:

• Functional stool testing (to identify pathogens, inflammation, and dysbiosis)

• SIBO breath tests (for bloating, IBS symptoms, or reflux)

• Food sensitivity panels

• Hormone and cortisol testing

• Micronutrient analysis

These tools help us personalize a root-cause plan that brings long-term resolution—not just symptom management.

The Takeaway

Your gut is not just about digestion—it’s where your whole health begins. Especially for women, tending to gut health is foundational for hormonal balance, mood, energy, skin, and immune function.

If you're experiencing symptoms that seem disconnected—from PMS to fatigue to breakouts—it’s time to start thinking gut first.

And if you want to learn more about how surprising symptoms might be rooted in your gut, be sure to check out Five Surprising Signs Your Gut Needs Some TLC, where I go deeper into conditions like anxiety, autoimmune disease, and hormonal imbalance and how they link back to the gut.

Because when your gut is well, you feel well.

Dr. Nicole Kearney is a naturopathic doctor who lives in Burlington, Vermont. She sees patients at her office in Burlington as well as clients nationwide via telehealth. She specializes in fertility, hormonal, thyroid, and gut health.